That's because the characters in your document are, in fact, input as 'a', 'b', etc. It's the original font that was used that's wrong.

You will find the epub export is correct if you replace the bad characters with actual alpha, beta etc.

The underlying reason is that fonts and private font encodings are not guaranteed to carry over into any/all epub documents. Character encodings, on the other hand, are; so if you input an 'a' you get an 'a'; and if you input an 'ɑ', you will get that.

Do you need a scripted solution for this? You can use the standard FindChangeByList script to replace a's with alphas.